RNA-Seq: differential expression analysis of controls (literature)

Libraries required

library(plotly)
library(dplyr)

Data

load("input/limma_SC_Controls.RData")
lab <- dea.limma

load("input/limma_SC_Controls_lit.RData")
lit <- dea.limma

load("input/limma_SC_Controls_lab_newSeq.RData")
ns <- dea.limma

logFC comparison

PND7/8 vs PND14/15

plot_logFC <- function(lfc1, lfc2, n1, n2) {
  library(plotly)
  library(dplyr)
  library(robcor)
  
  rownames(lfc1) <- lfc1$Genes
  rownames(lfc2) <- lfc2$Genes

  l1 <- lfc1[abs(lfc1$logFC) >= 1 & lfc1$adj.P.Val <= 0.05, "Genes"]
  l2 <- lfc2[abs(lfc2$logFC) >= 1 & lfc2$adj.P.Val <= 0.05, "Genes"]
  
  genes <- union(l1, l2)

  dat1 <- lfc1[genes, "logFC"]
  names(dat1) <- rownames(lfc1[genes,])
  
  dat2 <- lfc2[genes, "logFC"]
  names(dat2) <- rownames(lfc2[genes,])
  
  genes <- intersect(names(dat1)[!is.na(dat1)], names(dat2)[!is.na(dat2)])
  
  fit <- lm(dat2[genes] ~ dat1[genes])
  fitr <- MASS::rlm(dat2[genes] ~ dat1[genes])

  plot_ly() %>%
    add_trace(x = dat1[genes], y = dat2[genes], mode = "markers", name = "Genes") %>%
    add_trace(x = dat1[genes], y = predict(fit), mode = "lines", name = "lm") %>%
    add_trace(x = dat1[genes], y = predict(fitr), mode = "lines", name = "rlm") %>%
    layout(
      xaxis = list(title = n1),
      yaxis = list(title = n2)
      # title = paste("SC controls logFC:", n1, "and", n2)
    )
}

lit: PND14 vs PND7 & old: PND15 vs PND8

plot_logFC(lfc1 = lab$`PND8 vs PND15`, lfc2 = lit$`PND7 vs PND14`, n1 = "old: PND15 vs PND8", n2 = "lit: PND14 vs PND7")

lit: PND14 vs PND7 & new: PND15 vs PND8

plot_logFC(lfc1 = ns$`pnd15 vs pnd8`, lfc2 = lit$`PND7 vs PND14`, n1 = "new: PND15 vs PND8", n2 = "lit: PND14 vs PND7")

old: PND15 vs PND8 and new: PND15 vs PND8

plot_logFC(lfc1 = ns$`pnd15 vs pnd8`, lfc2 = lab$`PND8 vs PND15`, n1 = "new: PND15 vs PND8", n2 = "old: PND15 vs PND8")

lit: PNW8 vs PND14 and new: PNW21 vs PND15

plot_logFC(lfc1 = ns$`pnw21 vs pnd15`, lfc2 = lit$`PND14 vs Adult`, n1 = "new: PNW21 vs PND15", n2 = "lit: PNW8 vs PND14")

References

report::cite_packages(session = sessionInfo())
##   - C. Sievert. Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman and Hall/CRC Florida, 2020.
##   - Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2021). dplyr: A Grammar of Data Manipulation. R package version 1.0.5. https://CRAN.R-project.org/package=dplyr
##   - H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
##   - Paul Smirnov (2014). robcor: Robust Correlations. R package version 0.1-6. https://CRAN.R-project.org/package=robcor
##   - R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

SessionInfo

devtools::session_info() %>%
  details::details()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.4 (2021-02-15)
 os       Ubuntu 16.04.7 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Zurich               
 date     2021-06-25                  

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